Through the Mirror, Darkly
by Cutie Pie 9335
Summary: Post STID: When an alternate Khan appears, claiming to hold the key to saving the universe, James Kirk must form a tenative alliance with the deadly super-soldier to defeat a new enemy. Mirror!Khan/Kirk
1. Prologue

**Author's EDIT Note: I made a few minor changes, really no big deal. Carry on.**

**Author's note: Okay, so without giving any plot points away, I just want to remind everyone that this is a prologue and is totally not what you think. Next chapter, elaboration. This chapter, let the minor confusion take you for a ride.**

**Until then, happy reading!**

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Prologue: _The Final Frontier_

His lungs burned with exertion, his muscles ached from fresh bruises – but he would not stop. The metal briefcase tucked under his arm was a hefty reminder of what should come to pass should he not escape. Failure was simply not an option.

His own footsteps, muddled by the cavernous halls of the starship, blended with his pursuers, his captors, undoubtedly his would-be executioners. If they caught him again, not even the phaser on his hip would protect him from _His_ wrath.

_No, don't think. Run, just run. _

Essentially, he could run like this for hours without tiring – but that would be when he'd been at his peak. Weeks of malnourishment had left him gaunt, a shell of the man he's once been, and brutal sessions of torture had left him shaken, weak from pain.

The escape shuttle was 500 yards away.

Freedom was 499 yards away.

He pushed harder, willing himself to go faster. His blood roiled with exhaustion, his vision tunneled with the desperate need for more oxygen.

_Breathe. We're almost there. Breathe._

He rounded the corner past the engineering center, his prize finally in sight. A B-12 regulation shuttle, but this one was different. Week after arduous week, time had been spent making the preparations, upgrading the hull, re-outfitting the thrusters, sequencing long lines of transpondent-warp codes, codes that wouldn't be invented yet for years, perhaps decades. It was a model to marvel at – likely the most advanced ship in its time, and simultaneously a dinky escape-pod.

It deserved better.

Shots rang out all around him. Some of the lasers even grazed him, leaving behind seared trails in his black body suit, charring flesh and scorching blood on already bruised skin. He did not allow himself the leisure of passing out. Pain, he told himself, was just a momentary sensation.

He counted the seconds.

_Five. Four. Three. Two-_

An explosion tore a decent sized hole out of decks two and three, reverberating through the cruiser and rattling eardrums with its deep bass and solid _boom_. For a tense minute, the whole ship shuttered as life-support struggled futilely to generate more oxygen to compensate for the sudden loss of cabin pressure and exponential leak. The hangar lights dimmed minutely before the reserves kicked in.

"Status report now, I want ship-wide lockdown," the first officer's voice was sharp and loud over the sudden chaos of the ship.

_No, don't look back._

He was at the shuttle in an instant, throwing himself inside as quickly as possible and sealing the hatch. Gasping against a sudden swell of relief, he touched the metal walls between him and his tormentor. His other hand traced the ridges on the case; the easy part was over, now came the hard – actually escaping.

The controls were as he'd remembered, painfully simple as if children piloted these. It only took a minute before the communications were flashing; he engaged.

"—_You listen to me right now you goddamn son of a bitch, the bay doors are closed and that's exactly how they're going to remain. Surrender, or so help me _—,"

"As always it has been a pleasure, _James_," he hissed vehemently, suddenly feeling all his hatred rush to the forefront of his mind, "and I assure you if we ever cross paths again I will personally exterminate your entire crew. Alas, I have more important matters to attend to."

He terminated the transmission.

Just outside the hull, a certain first officer inwardly gnashed his teeth behind a façade of indifference.

"Sir, systems are malfunctioning," a nameless cadet blubbered, staring wide-eyes at a report tablet. The FO merely glared at the shuttle in response, attempting to school his features back into typical Vulcan passiveness.

A beat, and then, "Evacuate the loading docks."

"But, sir-!"

Spock stared coldly down his nose at the underling, silencing him with a look of murderous promise. He replied measuredly, "You have your orders. I will not tell you twice."

The Commander will not be pleased.

At the other side of the glass doors, the search party watched with horrifically grim expressions as their prisoner escaped. He'd planned perfectly, undoubtedly strategizing with an inside informant for months prior. The monocle failure, the bomb, the system virus. And now Spock would have to answer to the Commander for this breach of security, for this incredible obstacle in what had once been an air-tight plan.

As the shuttle disappeared into the vacuum of space, Mr. Spock decided to call it.

"Issuing warrant: red card, level 9, on escaped felon Khan Noonien Singh."

No, the Commander will not be pleased at all.


	2. Chapter 1

**Author's Note: Oh my goodnes, well here we go with the next chapter. Alright, so I'm not going spoil the pairings or anything just yet, so stick around and you'll see. T****hat having been said, I hope you all enjoy this next chapter and as always, reviews are much appriciated.**

**Happy reading!**

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Chapter 1: _What May Be Necessary_

"This is not how I imagined I would be spending our five year voyage."

Captain James T. Kirk fell into step with his Commanding Officer, brushing against his shoulder in an unmistakably familiar gesture. They carried on walking, passing various offices through the newly remodeled San FranciscoStarFleetControlCenter in comfortable silence.

Finally, Spock replied with a monotone, "The field scanner upgrade is a logical improvement."

"It's damn inconvenient."

"It is as you may call it a 'necessary evil'."

Kirk snorted, shooting a quick sidelong glance at the Vulcan.

"I think we're here for more than just an equipment and systems reboot. The Enterprise was in fine condition after her first overhaul. They're up to something."

"They?" came the tentative inquiry.

"Yeah – them. The brass, the upper echelon, Marcus' buddies."

"You suspect we are still under inspection?"

Kirk slowed until he came to a stop, fully facing Spock with a serious set to his jaw. "Think about it – it's been almost five months since we officially departed. What new upgrade could be so important to call us back all the way to HQ to get it replaced? Why not have us dock on a nearby Star Fleet colony?"

"Whatever you might be suggesting, Captain, it is highly improbable. The Admirals have no reason to mistrust neither you nor the crew of the Enterprise," Spock's impressive eyebrows drew together in a rare display of a facial expression.

"Then why are we here? Come on, I know you aren't buying this crap."

"I will admit our delay seems poorly timed –,"

"Three weeks!" the Captain exclaimed slightly too loud. His voice immediately dropped to a whisper, "We've been here already for almost a week, we still have two more to go. I've been dragged off to every Captain's dinner imaginable, stuck in every board meeting they can think to put me in. And Bones has been forced into some weird science/medical convention. God knows I've barely seen you for more than a few minutes at a time – they're watching us, Spock. I don't know why, but they are. We're being split up and observed."

"You are certain, verified by facts?"

Jim made a noncommittal sound, "You know I can't say that. But what I do know is that something's up."

The Vulcan let loose an uncharacteristic breath of exasperation before finally meeting Jim's eyes. "Until we acquire any tangible proof, your suspicion shall remain mere suspicion. We would require access to personal encrypted data files of administrative personnel to commence our search, a high offense if discovered."

"Is that an offer?" Jim asked lightly, his blue eyes twinkling with a playfulness the Vulcan was surprised to find he missed.

The pair rounded the corner into a wider hallway, consisting almost entirely of tall panned windows facing out onto the sprawling quadrangle. Cadets and various officers bustled in small groups between the buildings. Kirk couldn't help the smile that tugged at the corner of his lips – everyone seemed so caught up in what they were doing, and thinking.

It had been close to two years since the incident. Crashing spaceships and burning rubble were far from everyone's mind, however, Kirk thought with a grim note, history has a way of repeating itself. And while Khan might still be on ice, the fact remained that others equally dangerous still threaten Star Fleet and her officers. Not to mention the internal threats still abound.

Since the Marcus incident, Star Fleet had ensured it would keep a closer eye on her own, hoping to deter any would-be defectors. All they'd managed to do was royally piss off a few Admirals and confine a few Captains, Kirk himself included. Parameters had shrunk, command missives had grown lengthier – and Jim was ready to throw in the towel.

"It is a statement," Spock replied, bringing the Captain back to himself. He turned once more to continue walking but paused, only for a moment to toss over his shoulder, "One that will require you at the H-Block archive tonight, preferably dressed in darker attire."

Jim Kirk grinned in spite of himself.

"So, it's a date."

"It is an offer."

The smirk was clear in his voice, even when all Jim would see was his perfectly straight back and damnable pointy ears, retreating farther down the corridor until disappearing entirely around the corner.

. . . . .

"Spock!" Jim called out into the half-darkness, broken up only by the sallow light of the cityscape outside. The archive building had been easy enough to gain access to – nothing a small set of coordinated phaser bursts couldn't solve.

In a flash, a hand clamped vice-like down on his mouth while another arm held his shoulders barring any extraneous movement.

"Captain, noise higher than this current decibel is ill advised," came Spock's whisper, not much more than the mouthing of words over an exhale. Kirk nodded as his first officer's grip slackened until just one hand remained between his shoulder blades, gently steering him in the direction of a mainframe console.

The Vulcan moved like a cat, barely brushing against Jim's side as he turned on the large computer. The screen jumped to life and Spock set to work. He bypassed the sleek cover of the software with a few swift keystrokes, opting instead for the plain lines of code. His fingers glided with practice ease as he sifted through the mass amount of irrelevant information.

In the blue glow of the screen, Spock looked alien. At least, more alien than per usual, Kirk thought with a smirk.

"Captain, I believe I may have found something."

Jim leaned in closer, scanning the dizzying lines for tangible phrases.

"Project XI-9?" The words felt ominous aloud. Jim locked eyes with Spock for a brief second, sharing a strange moment before returning their attention back to the database.

"No prime directive is stated, but an impressive amount of credits have been allocated to it through untraceable wired accounts."

"So…?"

"So there are discrepancies in the released Star Fleet budget, according to the existence of this such project."

Jim let out a short huff, "Well, is there anything else here? Anything to give us an idea of what they're spending the money on?"

"Negative, Captain."

The last thing Jim wanted to do was let this go, but without anything further to go on, project XI-9 would remain just a top secret budget sink.

. . . . .

Doctor McCoy forced another smile as yet another fleet doctors passed by, thankfully he didn't stop for a long, insufferable conversation just to say _well, how about this weather, huh?_ For the first time, Leonard actually missed the hectic missions and panicked seconds as he worked to remove poisonous spines of Jim's arm, or stop the bleeding on a phaser wound, stab wound, internal puncture wound on Jim, or just generally keep his Captain upright.

Hell, even the damn awkward and annoying physicals on the hobgoblin were better than this.

He'd been stuck in this purgatory from the moment the Enterprise landed in the SanFran docking bay, dragged off to this ridiculous and never-ending convention where his peers hummed and hashed over his work, each expecting him to ooh and ah in return. His southern patience was running thin and he didn't want to spend another Kansas second here.

"Doctor McCoy?"

Leonard cursed, turning around to snap, "Oh for the love of -!"

"Bones!" Jim's whole face was alight with that mix of unadulterated joy and mischief.

"Jim!" The doctor, forgetting his foul mood momentarily, lurched forward to clasp his hand firmly around his Captain's forearms. He even flashed a genuine look of relief over in Spock's direction, who meanwhile stood impassive to the warm greeting.

"Please tell me the ship's done and you've come to bust me outta here," Leonard pleaded.

Jim shook his head, "Afraid not, Bones. In fact, we've come to –,"

"Doctor McCoy!" An older fleet doctor whipped around the corner, brandishing a data pad with one hand. "Have you had a chance to look over Millan's notes? His definition of 'cured' seems questionable."

Jim stepped forward, suddenly all formality and nearly oozing his Captain-vibe.

"I'm afraid the doctor's otherwise occupied right now," he said not unkindly but with authority enough to warrant the other physician to shake Kirk's hand and apologize profusely for his interruption.

"I could kiss you," Bones sighed in relief.

"Later," Jim said in a mockingly flirtatious tone. "Right now we have something more important to talk about. Come on."

The trio escaped the convention hall, moving in a pointed silence and with practiced purpose until they found themselves in an empty hallway, windows facing out onto one of the main courtyards.

"Have you ever heard of Project XI-9?" Jim asked finally, turning a critical eye upon his doctor.

McCoy thought for a moment before he shook his head, "No, I don't think so. I know medical has a few things under wraps but most have pretty straightforward names – things like Surgical Implant Procedures number seven. I mean, as doctors, code names are as useless as tits on a boar."

The three fell silent once more. Jim ran a hand along his jaw contemplatively, doing little to mask his frustration.

Just as the Captain opened his mouth to speak, a strange rumbling seemed to fill the hall, reverberating in the air and vibrating the very ground they stood on. Jim locked eyes with McCoy, surprise and suspicion flitting across his features.

"Captain," Spock said sharply, pointing out at the courtyard directly before them.

Light particles were amassing and swirling, forming a steadily solidifying shape about the size of a large hovercraft. For a moment, the shape seemed to shift, as if the object wouldn't quite fully make the teleportation.

And then, as abruptly as it had begun, it ended with an ear-splitting clap.

Sitting in the courtyard, steam and smoke swirling off its hull, was a regulation class shuttle, precisely a B-12, which had materialized out of thin air. For a moment, it seemed nothing would happen until the warning siren split the calm.

Without preamble, Kirk pulled out his phaser and shot the glass, breaking the window. Immediately he leapt through, his first officer and chief physician only steps behind.

"Was that necessary, Captain?" Spock asked over the chaos.

Kirk stared at the mystery shuttle down his sights as he replied, "As necessary as that scanner upgrade."

The trickle of Star Fleet guards was steady as they filed out of the surrounding buildings to form a perimeter, falling into line with Jim and his crewmates. Suddenly, the shuttle hissed as its main hatch was engaged, slowly lowering to reveal a silhouette of a humanoid figure, obscured by dim interior and backlighting of the ship.

"Come out with your hands above your head!" the Captain called out, tensing his grip on his phaser.

There was a beat, and then the figure raised his hands, stepping forward into the over-cast San Francisco sunlight.

Kirk forgot to breathe – he couldn't breathe, his lungs seem to shrivel as he released an outward gasp. His chest heaved, his adrenaline spiked, his senses went into overdrive yet he remained absolutely paralyzed with rage, with _fear_.

Those eyes.

Those damningly familiar blue eyes met his, wide with equal fear, with undeniable horror. Pure, aching _terror._

He never got the chance to open his mouth – two phaser shots struck him square in the chest and he crumpled. No fight, no proclamation of victory or of unspeakable genocide, not even a taunt.

Khan Noonien Singh was lying unconscious at Jim Kirk's feet.


	3. Chapter 2

**Author's Note: Alrighty! This was a quick update but I was struck by the muse. I'll keep it short - thanks to everyone who had followed and favorited, a big thanks for those who've reviewed - you guys make it easier to write chapters - and thanks to everyone else who has read this story so far and given it a chance.**

**Enjoy.**

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Chapter 2:_ First Time for Everything_

"How the fuck did he escape?" Kirk shouted right into the face of Admiral Tesius, essentially the highest authority the Captain could find to yell at.

Spock put a calming hand on his captain's arm yet did little to actually stop him.

Immediately after Khan had stepped from the vessel, Spock fired twice in rapid succession, hitting his mark perfectly with little mercy. Had he a moment to truly consider, Spock realized he should have switched his phaser to kill, but reaction had gotten the better of him, and Khan had lain motionless on the concrete, chest still rising, heart still pumping.

The guards swarmed the prone body, dragging him off to a holding cell where he would undoubtedly be transferred back to his cryo-tube as soon as possible. Jim, however, staggered backwards, struggling to get in even one breath. His wide eyes found Spock's own, complete disbelief reflecting the Vulcan's feelings tenfold.

Everything was far off, voices blending into just one massing rush of noise. Jim sank to his knees, phaser falling from his limp hand, as McCoy leaned in to take his pulse. Over the roar in his ears, Spock could here the doctor telling him to breathe, _damn it Jim, just breathe._

Without another thought, Spock kneeled before Jim and placed his fingertips along the side of his friend's face. Tranquil, clear, collected. Spock reined in Jim's panic with his own thoughts, soothing the wild beast of traumatic stress with his own mind, careful to mask his own emotions.

The very moment Spock saw reason, sharp and resilient, flash through Jim's eyes, he knew there would be no stopping him. Ignoring Leonard's pleas to sit back down, Jim stormed into the administrative building and demanded to see someone, anyone, to get some answers.

Spock had to give Admiral Tesius credit – for a man who had never served in anything notable, he handled the situation with all the pomp and solemnity possible. He'd assured Jim that no such escape had occurred, and that if such had, he had no knowledge regarding the situation other than that the situation would be handled swiftly and with great prejudice.

In fewer words, Tesius was ignorant to any facts and negligent to his responsibilities.

But in the end, there was little to do other than continue to shout obscenities at the Admiral and so they had been escorted to another area, likely as far away from Tesius as possible, lest Kirk think of new insults to hurl at the man. They could do little more than wait until command had results to actually report.

The wait, it seemed, was short-lived.

"Mr. Spock," a cadet addressed him, saluting briefly before approaching him. Jim instantly perked up, sitting straighter in the chair he'd been provided. "We recovered something from Khan's shuttle that we'd like you to come take a look at it."

Kirk jumped up as if to follow, but the cadet then turned to him as she continued, "Captain Kirk, the fugitive is now awake and in the interrogation chamber of Block C. They are requesting your presence. Yours too, Doctor McCoy."

There was no hesitation in Jim's step as he darted off down the nearest hallway. He sprinted to the cell, his brain a whirlwind of various thoughts, yet he kept coming back to one. _How?_

Khan had been frozen, sentenced to forever as an ice cube. There was no way he could have gotten out, unless someone let him, unless it had been a backup plan from the beginning. It wasn't in inconceivable thought, but why had it taken so long then? And why beam back down to the same area he got taken down at?

He'd been so caught up in his analysis, Kirk almost didn't realize he was already there until he ran nearly head first into the security guards posted outside. Anxiety built in his gut as he neared the chamber, winding down a few stairs until he'd reached the right floor.

In the following room, an unbreakable glass shield occupied an entire wall; the other three were made of solid concrete, broken up only by a single, heavy metal door on one side. The room was bare, spare the only furnishings which were a metal table and a chair, both fused to the floor below.

And Khan.

The bastard's gaze was trained on the floor, his face a careful mask of practiced indifference. Kirk studied him intently, soaking in every detail as if it might tell him how in the world Khan had gotten out.

A deep purple bruise adorned one of his sharp cheekbones, stretching all the way up his temple and disappearing into the matted mess of his hair. It seemed slightly shorter than before, and infinitely dirtier, as if Khan hadn't seen a shower in months. A faint cut sat on the center of his bottom lip as if it had been previously split and not quite given the chance to heal. His eyes were rimmed with red, a sign of stress combined probably with a lack of sleep, if the bags under his eyes were any indication.

Khan seemed to slump inward on himself, like sitting up straight would require too much effort. Like all he could afford to do was breathe. His clothes were nearly identical to before – simple tight black shirt, simple tight black pants, and black combat boots. But unlike before, they were dusted with a fine layer of dirt and torn slightly in places. One tear ran across his arm, as if he'd been skimmed by a laser shot: the clotted wound underneath seemed proof enough.

In short, Khan had the shit beaten out of him. By who?

Kirk made his way over to the door and mentally steeled himself for the encounter. Khan had a way with words, weaving truths with lies in an ungodly deep voice.

When the door opened, Khan didn't bother to turn around. When the door slammed shut, Khan didn't show any reaction. When Jim stood in front of the war criminal, Khan didn't look up. Khan sat perfectly still, either lost in thought or pretending to be.

"Here's how this is going to work: You're going to tell me how you got here and then, you're going to continue answering for your crimes," the Captain said in an even voice. This time, Khan reacted, but almost violently.

His head jerked up and wide, dubious eyes watched him like a caged animal might match its captor. The look seemed so wholly out of place that for a moment, Kirk felt a stab of guilt in his gut, for what though he had no clue. However, his poker face slowly slid back into position, his face relaxing again into passiveness.

"Captain James Tiberius Kirk," Khan said the name slowly, as if tasting each syllable. Those eyes bore into his intently. "It's a pleasure to finally meet you."

. . . . .

"Its contents are unknown. Its locking mechanism is unknown. Its alloy is unknown. In fact, the only thing we do know is that it's a case of some sort that may or may not be booby-trapped."

The Head of Security shot Spock an expectant look before flipping her curls back over one shoulder. She was a bull of a woman, all thick thighs and synched waistlines, but her soft facial beauty belied the stern attitude she expressed.

Spock nodded, pushing up his sleeves as he stepped forward to the briefcase, laid out on an equally sterile-looking exam table. The pulse in his temples throbbed with the start of a migraine, a rare occurrence for Vulcans.

Lightly, he ran his fingers over the smooth surface. It was cool to the touch, obviously a metallic substance but not one readily identifiable.

_Meaning it may be a special compound_, Spock thought to himself. Suddenly, he fiercely wished for the doctor's company or even Carol Marcus' opinion. Anyone with whom he could bounce ideas off of, brainstorm the best way of going about this dissection safely.

Doing any sort of experimentations on would be highly dangerous without any knowledge as to what may be inside. This predicament would require either entirely too much precaution to glean any information or necessary risks, as Jim so called them, would have to be exercised.

It was going to be a long night.


	4. Chapter 3

**Author's Note: Okay, here comes the next chapter in this series and I hope everybody enjoys it. I just wanted to thank everyone who has favorited, subscribed to, and generally just read this. An extra special thanks to all the reviewers who take the time to give those words of encouragement, thank you so much! Your kind words mean a lot and they give me the motivation to update. Basically thanks everyone!(:**

**Enjoy!**

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Chapter 3: _Dammit, Jim_

McCoy could have screamed – in fact, for a moment, he seriously considered it. He could've screamed at the guards, yelled at Jim for his recklessness, and then not wasted a breath on Khan because tell him he's a despotic asshole and he'd probably just smile.

And maybe McCoy was still oddly grateful for the super human. At least for his existence, in any case.

"Jim?" the doctor called out over the intercom linked to the cell. His captain looked tense and judging by the muscles coiling on his back, he looked ready to snap. No one had ever managed to get under Jim's skin the way Khan had, except maybe the hobgoblin on occasion.

He should have waited, but being Jim, he'd rushed in.

The Captain walked back towards the door in a falsely calm manor and Khan just sat there, watching him with a flat expression. There was no typical smirk of victory, no look of sadistic glee, not even the grim yet calculating stare as if he were plotting an escape. Khan looked almost genuinely surprised and then, strangest of all – he looked relieved. A breath the madman had been holding rushed out of him and his body momentarily went limp.

"Jim! For god's sake man, you should have waited –," McCoy set into his Captain before Jim held a hand to stop him. The blonde looked rattled.

"He said it was nice to meet me, Bones." Blue eyes sought his, endless in their questions. "That man, whoever he is, it's not Khan. It's not the Khan we know. I don't know what happened to him, if he forgot everything or if he's just playing me. I don't…"

Jim trailed off, unable to finish his thought.

"Go for a walk. Clear your head." Bone placed what he'd hoped to be a reassuring hand on Jim's upper arm. "I've got some medical stuff to take care of down here with the diva. Boring, routine stuff. I can send for you when I'm done."

The Captain's eyes slid back to the criminal mastermind, something stirring deep in those cerulean depths, and then refocused back on Leonard as he said, "I'd rather stay, Bones. I'd feel better keeping an eye on you myself."

For once, Bones didn't argue.

. . . . .

If Khan had looked alarmed when Jim had stepped in, he looked downright uncomfortable as soon as Doctor McCoy stepped through the door. His striking blue eyes followed each movement of the doctor almost obsessively, as if his life depending upon watching each minute twitch. As if he had learned his lesson about not watching.

"Khan Singh, alias John Harrison," Bones read aloud from the profile PADD the chief of security had given him. "Height: 6'0" – Weight: 175 lbs, give or take. Eye color: blue; hair color: black. IQ: indiscernible."

Softly, Leonard set the tablet down on his side of the table, finally facing the veritable thorn in Star Fleet's side, yet also the unintended savior of his captain. He sat himself down on a chair which command had so generously provided, thankfully not bolted to the stone floor. Interrogations were not Leonard's strong point, hell he had a hard enough time making small talk with the _Enterprise__'s_ crewmen.

Bones let out a rough sigh, running his hand across the stubble gathering at his jaw.

"The blood sample I snagged from you while you were out cold suggests that you are in fact the real Khan, and until the boys send back word of the cryogenic tank you're supposed to be locked in, we're going to assume that you are who you say you are," Leonard drawled slowly, keeping steady eye contact with the prisoner. He expected Khan to remain silent, steely in his resolve to not speak.

What Leonard did not expect was for Khan to smile.

Pleasantly.

"Doctor," Khan grinned, a fleeting faint little movement at the corner of his lips yet the action absolutely lit up his too-blue eyes. Even his tone was different, polite and not dripping with the superiority it once so viciously held. He continued almost conversationally, oblivious to Leonard's apparent dismay, "Good morning. I hope my unannounced appearance hasn't caused too great a stir."

"What?"

The word fell ineloquently from Leonard's lips, the southern doctor unable stop his astonishment from his features.

Khan balked slightly, "I am aware that I wear an unwelcomed face, but I had thought I might have been able to avoid creating such a panic. Unfortunately, I haven't a way of contacting you ahead of my arrival so I took a chance, a leap of faith if you will. Luckily for me, your courts uphold fair trials."

For a moment, Leonard didn't have a response. In a round-about way, Khan was apologizing for making a scene, apologizing like they'd never met, or if they'd had it was on some formal occasion – apologizing like he hadn't tried to kill the entire Enterprise, murdered Admiral Marcus, and dropped a spaceship on San Francisco, the very base he just popped up in.

Khan Noonien Singh just said he was sorry.

And all Leonard could say was, "It's not morning."

To his credit, the psychopath had the decency to look confused before McCoy could recover.

"It's night," Leonard let his eyes rest on the data PADD for a moment before gathering up enough courage to meet those twin cerulean depths once more. "Right now, it's close to midnight."

"Oh," Khan blinked, actually looking disoriented as he took another look around the holding cell, as though he were truly seeing it for the first time. The awkward silence was a deafening roar, yet Leonard could only think how he liked it a lot better when Jim was yelling the Admiral and Khan Noonien Singh was a distant anomaly, a freak incident ensured to never happen again.

Leonard repressed a sigh and ran a hand through his hair. Some people have all the luck.

"I need you take your shirt off."

Khan looked alarmed and then suddenly, that polite demeanor vanished. The light in those blue eyes died, closed off with a severe resolve covering a simmering wash of fear.

"I only need to run a couple tests," the doctor hastily added, showing his palms as the international 'no-harm' sign. "Only a few scans, take some biometric readings – nothing painful."

The fugitive relaxed, and as quickly as he'd changed, Khan flipped the switch back over to the courteous, non-threatening man he'd been seconds prior. It was eerie, Leonard thought, watching the pulse jump under the skin of Khan's neck. It was also reactionary.

"Of course." Another smile, now looking a little forced around the edges.

In one swift choreographed motion, Khan pulled the shirt over his shoulders and head with both hands bound, working it down until it was bunched, inside-out, at his wrists.

It was practiced, a movement repeated several times under identical circumstances. Meanwhile, Leonard tried, and failed, not to gasp at the sight of the newly revealed skin.

Bruises dotted his arms, in either dark, deep pits of broken vessels indicating blunt force trauma or thinner, spindling discoloring formed by ropes or powerful hands. Fresher, still-open wounds tarnished his biceps, looking suspiciously like phaser marks if the charred gashes were any indication.

And that was just his arms.

Doctor McCoy was hesitant to see the rest of Khan's back, feeling at once squeamish and yet sorry for the madman. Someone had certainly intended him pain, and copious amounts of it.

"Who – err, how did this happen?" If McCoy's voice shook, no one mentioned it. If Khan refused to meet his eyes, it went unnoticed.

The doctor hesitantly moved from his spot to get a better look at what he knew would be much worse injuries. Khan, as always, did not disappoint. Long scars from whips of some kind raked down his back interwoven with even more extensive bruising and blistering, painting a gruesome tale of torture.

"You," the word escaped like a barely breathed concession, so fleeting and soft that for a moment, Leonard was certain he'd simply imagined it. Yet, before he could ask, Khan slipped his shirt back on easily, concealing the horrors of his body.

"Thank you for your time, Doctor, but I can assure you I am fine," Khan's voice seemed to drop deeper as he fixed his attention fully upon Leonard.

"Fine?" Leonard snorted in spit of himself. "And I'm a monkey's uncle. You need medical attention, damn it. Real medical attention, not just me eye-balling your boo-boo's."

"Regardless, I do not require-,"

_Smack!_

"I'm not asking!"

Leonard's hands were shaking on the table top where he'd slammed them down. The Georgian doctor was used to occasionally having to push patients into complying with practical medical procedure, namely a blonde captain with a bit of an unlucky streak, and kowtowing to a certain mouthy Vulcan.

But bigoted psychopaths?

He was admittedly not well-versed.

Khan didn't reply, didn't do anything other than stare intently at the floor, his face back to that impassive, unreadable, damnable mask of indifference.

"I'm going to schedule you to be moved to the biomedical cell so we can at least patch you up and check for internal bleeding," Leonard sighed, picking up his PADD as he turned to leave but he hesitated in the doorway, feeling a strange rush of misplaced guilt and duty. Tossing over his shoulder, he added, "And if you need anything, all you've gotta do is ask. Preferably nicely."

The door slammed shut, with locks engaged.


	5. Chapter 4

**Author's Note: Oh my goodness, technically we're on Chapter 4 and I'll admit that I sort of broke this chapter in half. There was a certain point where I felt like if I kept the chapter going, it would disrupt the flow and so then I just decided on a whim to break it into two parts, but on the bright side, hopefully that chapter will be out much sooner. I'm working on getting a day set that I can update regularly on but so far, in my hectic little life, I can't quite find the continuity so thanks, so so much for all your great patience with me and my sporadic updates. **

**Thanks to everyone to favs and follows, also to those who read. Extra special thanks for all those lovely reviewers who take their time to give me words of encouragement or advice, thanks so much (: Please enjoy!**

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Chapter 4:_ This Breakable Tryst_

Spock read the message twice.

It was illogical – he had read the brief paragraph in 2.7 seconds and retained the knowledge it held. Reasonably, Spock understood the message with perfect clarity. Yet he read it again, staring at each word for an inordinate amount of time as if they might suddenly rearrange themselves into what the Vulcan had expected.

No such phenomenon occurred.

Spock read the message for a third time through, allowing himself a momentary slip of physical emotion as a frown pulled at the corners of his mouth.

_Commander Spock – Your requested the data on the cryogenic tank number 00B1, occupant: Khan Noonien Singh. All vitals remain unchanged, all biometric readings remain unchanged. Brain activity is nominal in regards to deep-freeze state. The tank has remained in the sealed vault since first enacting Khan Noonien Singh's sentence. Thank you for your time and if we can assist you further, please contact the officer's help center with your personal identification number._

Khan was frozen.

Khan had _remained_ frozen.

Spock read the message a fourth time.

. . . . .

"Just who _the hell_ are you?"

Jim Kirk was a man on a mission.

But that was after.

It had been only moments ago that he'd been dragged off to the deserted dinning hall, browsing through Scotty's typical and thorough analysis of _The Enterprise's_ system and scanning the section about warp-core capabilities again. In some way, the objective report was cathartic, soothing to the Captain's otherwise frazzled nerves.

Familiar vernacular had filled his mind – _warp stabilizers, dilithium inhibitor, transient-ascension cables._ If only the world was like his ship, his _Enterprise_, where everything had a categorized duty, clearly labeled and functioning. Nothing was irreparable, everything was practical.

There weren't any unexpected visitors, certainly not any fraudulent psychopaths with a penchant for manipulation and exploitation.

Jim had set the PADD down for a moment to quietly regard his Chief Medical Officer who had grown increasingly morose and furrowed with each passing second following his interaction with Khan. Of course, the Captain had watched the whole exchange.

And of course, Jim could practically read Bones' thoughts as if they were written across his pensively wrinkled forehead. It would only take a few more seconds.

Khan clearly had been held captive, undoubtedly inflicted pain for whatever reason – likely information or knowledge, probably not entirely different from what Admiral Marcus had wanted. And what's more, Khan had been tortured _extensively_. The super-soldier could withstand a solid beating and regenerate inhumanly fast, which meant that his tormentors were either impressively determined or strong beyond measure.

In this case, Kirk suspected it was both.

And yet, Khan had managed to escape, popping up on their doorstep without as much as a hello, a very different choice of hideaway. However, everything about the fugitive was already markedly different, his attitude, his behavior, hell even the way he _breathed_. Each exhale seemed somehow less pompous and more guarded. It was strange.

"Something's not right, Jim," McCoy predictably broke the silence, as if he'd telepathically tracked Jim's own countdown. "Khan's not right. I don't know what it is, and shit, I'm not even sure I want to know. There just ain't an explanation for it."

"I may have one, Doctor."

Spock slid calmly into the space on the bench next to Jim, looking grim underneath that practiced poker face. Mutely, the Vulcan passed the Captain his PADD, his dark eyes scrutinized Jim as he read the fateful message.

All color drained from Jim Kirk's features.

"Well?" Bones prompted impatiently.

Kirk had simply stood up and darted off in response, running almost on auto-pilot as he weaved his way back to the holding cell. No one stopped him, no one questioned him as he'd thrown the door open and planted himself firmly in front of Khan, both hands splayed on the tabletop.

"Just who _the hell_ are you?"

The Khan-imposter just stared, for a moment as though in shock, but then it was replaced with an eerie calm. He started haltingly, "Captain, I realize this may –,"

"_Shut up_," Kirk seethed. "Who are you?"

There was a pregnant pause as the two men stared each other down.

The Not-Khan broke eye contact, releasing a stuttering sigh before finally returning his imploring blue eyes up at the Captain.

"I…," a deep breath and then the confession came, slow and deliberate, "…am Khan Noonien Singh. But I am not _your_ Khan Noonien Singh."

Kirk arched an unimpressed eyebrow.

"No doubt you are aware of the existence of parallel universes," Khan spread his hands, palm up, as wide as the manacles would permit.

"Imagine one solely perpendicular, opposite to all you know in every minute way. In this universe, the name Jim Kirk belongs to a respected captain, endowed with mercy and courage beyond his years," Khan paused as something dark gathered in his being, those hardened eyes locking onto Jim and looking all too familiar, "but in my universe, James Tiberius Kirk is a power-hungry tyrant, intent on enforcing his will upon the weak."

"And while this world's Khan is a despotic madman, you're what?" Jim crossed his arms and allowed some of the tension to leave his frame, "A hero? A saint?"

"A peace bringer," Khan offered instead.

Jim tried to not visibly flinch at the words.

"I was made, built to be perfect specimen of humanity by the Eugenics Project and destined to bring harmony to the universe," Khan sighed again, reclining in his chair. "But in the world I come from, peace and harmony are not goals so widely sought after."

"So why are you here?"

At this, Khan's gaze flittered across the Captain's features, as if in turn searching the other man for what, Jim wasn't sure. His stomach clenched under the mutual inspection – a simple look from this man had him pinned and holding back tremors. Even without being the same psychopath from all those months ago, this Khan still had the same power to unnerve Jim Kirk, to disarm him with little more than a blink, or a twist of his lips.

Finally, Khan continued, "I became a liability – I was being used to achieve goals that are contrary to my moral understanding, and largely against my will, so I escaped. I came to the last place they could reach me, unarmed and seeking only refuge."

"Then tell me about the metal case."

If Jim felt any sense of satisfaction over the completely horror-struck look on Khan's face, well he probably would've admitted it. But hesitantly, and with much faked remorse.

Though to his credit, Khan recovered quickly and that shock turned to pure desperation as he bolted up from his chair with a speed and force that had the Captain reaching for his phaser before the other man had even opened his mouth.

"Have you touched it? Have you opened it?" Khan blinked rapidly, as if realizing something. "You haven't opened it. Where is it? What have you done with it?"

Kirk forced his hand back down, slowly uncoiling his body from his ready-to-strike position, and focused briefly on returning his heart back to a normal pace. Khan's sea-gray eyes pierced him with such ferocity, not so unlike the man Jim had dealt with all that time ago.

"It's safe," Jim said slowly, "but I want to know what's in it, and why you brought it here – because if it's dangerous –,"

"It's exceedingly dangerous!" Khan extrapolated, his brows pulling together.

"And you brought it here?"

"I had no choice!"

The frighteningly blue gaze slipped past Kirk briefly, boring down hard into the glass wall over his shoulder. Suddenly, something passed over Khan's face – uncertainty, confusion – followed just as rapidly by strangely terrified understanding.

And then action.

Before Jim had the chance to fully react, Khan had lunged forward, eyes still glued to the glass wall intently yet his hands still found their mark at his collar, grasping the material fully in his shackled fists. Time slowed and then Jim was being lifted off of the ground.

Had he a moment to consider it, Khan's lithe body which belied its strength and power might have impressed Jim Kirk. The agility which Khan could demonstrate combined with all that lethal power was even more impressive. Yet more impressive still, Jim would later think, was how Khan had managed, in one fluid motion, to lift Jim from the ground and leap simultaneously into the air, high enough to perch the arches of his feet against the metal tabletop.

In that one instant, Khan seemed to be defying gravity.

And then with an ear-splitting screech of metal against concrete, Khan – and subsequently Jim – were complying once more.

The table had been torn from its bolted footing from the floor, two of the feet popping clean off while the other two closest to the glass became a twisted angle of metal. _Khan_ had torn the table from its bolts. By doing little more than jumping up and kicking his feet out at the edge.

Meanwhile, as the table met its untimely demise in one direction, Jim found himself being pulled in the other, clear over the dismantled table and straight into the solid body that was Khan Noonien Singh.

The super solider, much like a cat, seemed to arch midair enough to maneuver both of them sideways, forcing Jim to instinctively curl inward on himself and brace for an impact that never really came. Khan had pulled Jim in such a way that he shouldered the landing alone, shielding the captain's body with his own.

Altogether, the movement had taken a couple of seconds.

Jim had lain there, back pressed against the cold underside of the table, and stared without seeing the blackness of Khan's torn tunic. Mind blank, nothing going through his head other than the rush of a heartbeat in his ears. It was _his_. In that instant, he realized the heartbeat to be his own.

In that instant, the room exploded into flames.


	6. Chapter 5

**Author's Note: Alrighty, next installment of this series and you guys have been incredibly patient with me and this plot! I just wanted to say thank you so much for all the reading, follows, favorites and as always the lovely reviews that absolutely make my day. It means alot hearing what you all think about what's going on. So, we're getting into it, the plot is thickeing bit by bit. But to be honest, this story will probably be pretty long, I have an idea of what I want to happen in my head and I'm just going to keep writing until its out there.**

**Anywhosies, thanks again for all the love and support(: Please enjoy this next chapter!**

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Chapter 5: _Bracelets and Chain Gangs_

_"Jim."_

Time became fluid, slipping through fingers and past the grips of consciousness.

The world swam, sounds and touches breaking through each cresting wave.

Fingers.

Fingers dove into hair, dug against scalp, sought out a pulse. Air skittered and danced in flowing breaths.

Wisps of thoughts ghosted over the surface of perception and scattered, rolling in every direction away from the center like errant marbles. Perfect crystalline yet flawed minutely.

Whiteness.

Light.

Light that was soft, corporeal, light that had hands that could touch, and caress, and pull, and shake, and lift. Light that had shape and form and shadows and _cheekbones_.

_"James."_

And a mouth.

The world began to tilt on its axis.

The world became dark.

. . . . .

"He'll be okay, you know."

Spock didn't turn around. If anything, the grip on his forearms which were folded seemingly calmly behind his back tightened. For a moment, Leonard McCoy allowed his hand to hover over the Vulcan's shoulder, dangerously close to physically comforting the alien.

There were times where Leonard saw the friendship between Jim and Spock plainly – two colleagues who cared about their work and worked well together. And then there were other times. Times like this one where Spock was emotional but trying not to be, where Leonard thinks back to that time at the volcano and thinks that he'd been wrong.

Spock would've saved Jim.

Not because he's their captain or a good man, but because for whatever reason, the same reason Leonard supposes he puts up with this crap, Spock _cares_. Spock cares about Jim and fiercely wants to protect him.

Leonard had seen the sentiment, unmistakable and evident written all across Spock's features when the bomb had gone off. Worry was etched into every hard plane of the Vulcan as he went sprinting down the hall, Leonard himself fast behind. It sent tremors through Spock's otherwise steady body as they made their way through the smoke and debris. It simmered under a refined mask when they'd found them – a bloodied Khan lifting an unconscious Jim when by all rights, they ought to have died.

Hours later, the Vulcan was still trembling faintly, so minutely that Leonard was sure he was the only one to notice. Hours later, and Spock was still watching Jim's now sleeping form from beside his hospital bed.

_Again_, a dark voice whispered in Leonard's mind. Déjà vu could be such a bitch.

Leonard let his hand fall back to his side.

"Security sent over the details," Leonard stepped forward, even next to Spock at the bedside, and offered a data PADD. "It was an attempt on Khan's life by an unknown assailant. A small, directed blast – not meant to kill anyone other than those in that cell block."

Spock took the tablet silently, mulling over the security feed up until the blast knocked out the cameras. It showed the same grainy pictures looped: one had the bomber, arming the device up until its explosion while the other had Khan and Jim, arguing until Khan pulled the captain over the table, kicking it down for a make-shift shield. Then fire, then blackness.

"What is the captain's recovery time?" The words seemed forced, coming from Spock.

Leonard half-shrugged, "I'd wager not long. He doesn't have any serious injuries, only some bruising around his back and ribs, a concussion from the force of the blast. I gave him something to keep him under just for a bit longer, but he'll come around in an hour or so."

Spock nodded, eyes never leaving Jim's placid face.

For coming from an explosion, Jim looked half-decent still – Leonard tried and failed to not marvel at the fast acting of the super-soldier, and also how perfect Jim's hair still was. Other than the slight dusting of pink across his cheeks and nose, a low-grade burn from the explosion (something really more akin to a sunburn) and the bruised discoloring over a small cut on his eyebrow, Jim looked fine. Better than usual, actually.

"Doctor, I believe you have another patient to look after," Spock said, breaking Leonard from his thoughts.

"Well, that's the kindest way I've been told to get the hell out," McCoy grumbled sarcastically, but knew the Vulcan was right. He'd detoured to Jim's room on his way to deal with Khan, but had yet to actually see the super-soldier. Not entirely a visit he was looking forward to.

Leonard left the mute alien, and their unconscious captain, alone.

. . . . .

Khan looked awkward.

For a man who had just brilliantly saved the life of one of Starfleet's finest, he appeared quite gauche. In his new medical cell, surrounded by even more security, Khan seemed like a dark and fidgety stain in the sterile white room, folding and refolding his hands across his lap.

Leonard braced himself, and stepped inside.

Ice blue eyes immediately trained upon the doctor and Leonard would have sworn all the blood drained from that already pale face.

"Good news, you're going to live."

Khan had the decency to at least smile dimly at the poor joke and Leonard decided that he liked this Khan much more. Assuming this was not the Khan they'd dealt with before, going by the conversation between Kirk and Khan before in the cell. Because the way Khan glanced about the room like he was expecting literally anything to leap out at him was absolutely not normal. And the smiling thing. Leonard was still trying to get used to that.

"How is Commander Kirk?"

Leonard kept his face carefully blank. _Commander?_ He wanted to ask, but opted against it, saying instead, "Jim's fine – nothing major but some cuts and bruises. He'll be sore when he wakes up, but he'll also live to be blown up another day."

Khan relaxed markedly, staring down at his opened palms quietly as if consumed by private thoughts.

"But," Doctor McCoy braved a few more steps closer to Khan and his place on the cell's gurney, "now that Jim's taken care of, I need to make sure you get squared away."

Directly after the explosion, after Jim had been whisked away from the fallout, Khan had been swarmed by security once more, shackled again and tossed into a new cell, the exact one that Leonard had requested he be moved to for a medical examination. Leonard felt more at home in the sterile environment, Khan however seemed like a cat about to be dunked in water.

Only this time, Khan simply went along with procedure sans protest.

Leonard remained stoic as he set to work on the supposed-criminal, setting in first on his back, the worst injury and now just a mess of burnt skin. It seemed he'd taken the brunt of the explosion.

"Does this hurt?" the doctor asked, rubbing the biomed salve on gently with gloved hands, cutting away the other pieces of dead flesh. The burn was intense enough that it had nearly scorched away all of the previous scarring, and thankfully, Leonard could heal this wound properly to allow for no scarring whatsoever. Small victories, he'd like to think.

"No."

Khan seemed determined to remain morose.

"You're one lucky son of a bitch," Leonard started.

"Or skilled."

Was that a wry response?

Doctor McCoy barked out a sharp laugh, "Or both. You know, saving the captain put you on a lot better footing with Starfleet. They might just believe that alternate-universe story."

"Then these are simply for show?" Khan held up his wrists, strung together by admittedly delicate looking handcuffs with an extra long chain between the two. With little more than a flex, Khan could snap them easily.

"Something like that," Leonard smeared another generous portion across the blistered skin. Silence threatened to descend once more but Leonard was struck with a sudden bout of bravery and curiosity. "Why _did_ you save Jim? Even point blank, you would've survived the blast."

"Would you not do the same?" came the baritone reply.

"Yeah, but that's not the point."

"Then what is?"

Leonard fell silent as he reached for the roll of bandages. It felt like a crude method of healing, but the old ways were still best for this kind of burn. Plus, knowing Khan's regenerative abilities, it would be gone in another few days.

"You're just different, I guess, from what I'm used to," he frowned, rolling the gauzed over his lower back and around his abdomen. The conversation lapsed until at last the doctor had finished his work and was preparing for another scan, until Leonard thought they were done speaking.

Then, Khan replied, his voice quiet but strong.

"Indeed, so are you."

. . . . .

"Captain."

Jim wasn't overly fond of being greeted in such a blasé manner by his first officer, especially after clearly surviving some sort of explosion. For a moment, Jim just closed his eyes against the bright lights and sorted out his body, identifying where it hurt and to what degree.

Ribs: Bad.

Back: Bad.

Left Leg: Bad.

Head: Bad.

Overall: Still alive.

"Mr. Spock," Kirk managed, opening his eyes again. This time, the world remained in its upright position. The hospital room wasn't much different than the one he'd been in months ago, only now he didn't feel nearly as groggy and he was still in his dirtied command uniform.

"An attempt was made upon the lives of both you and Khan, the bomber did not survive," Spock inclined his head slightly, taking a couple steps closer to the bed. "He and the other guard he incapacitated are both dead, the only casualties of the incident."

Jim nodded, fixing his gaze upon the opposing wall. The 'other' Khan had saved his life, not necessarily something he was all that happy about, but if anything, it proved his innocence. Or maybe it didn't. Maybe the entire thing was staged so as to make Khan out to be the hero.

It seemed entirely too convoluted, but Jim's mind still reeled silently with possibilities. In fact, Jim could have gone on thinking and reeling and supposing for a good long while if Spock's quiet question hadn't snapped him back to reality.

"Are you…well?" The Vulcan asked tentatively, now standing directly beside him flush against the mattress. Briefly, those long fingers twitched as if they might check Jim themselves.

Jim tried not to let his shit-eating grin show.

"Yeah, I'm good. Banged up, but I'm good," Jim patted the back of Spock's hand who in turn, didn't pull away from the impromptu touch.

If Spock smiled fractionally, neither of them mentioned it.


	7. Chapter 6

**Author's Note: Alrighty, we've got ourselves the next chapter. I'm pleased on how this has been turning out and I know it's kind of been going slow. You guys seriously are the best for being so patient and wonderful with me. I honestly haven't much idea on the timing, it's always somewhat of a surprise what ground I cover each chapter, so just buckle up and come along. Also, sorry it took _forever_ to upload this chapter, I ended up putting out three other chapters on my two different stories, so I've been rolling on those and being a tad neglectful.**

**As always, thank you for everyone who has read, followed, and favorited. Extra special thanks to all those lovely reviews who take their time to leave a few words of encouragement, your input really does help, believe it or not. **

**Please enjoy(:**

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Chapter 6: _The Start of Something Strange(ly Wonderful)_

Two days was much too long to spend in a hospital bed.

One day was pushing it, but two? Well that was simply unacceptable.

"Please Spock!"

"You require rest, Captain."

"_Please_."

"No."

"Spock!"

"Jim."

Captain Kirk flopped back down against his sterile bedding, groaning to himself and his likely more-than-annoyed first officer. The Vulcan was being absolutely stubborn, which at first had been kind of endearing, what with him bringing Jim whatever he asked for and playing countless games of chess, all the while insisting that he not move a muscle.

But now, after two solid days of grape juice and checkmates, Jim was bored out of his mind. And Spock wouldn't even let him win a game – each win Jim got was hard-earned after a grizzly struggle and kamikaze strategy too random for even the Vulcan to calculate.

"Seriously," Jim sat up enough to look his first officer in the eyes, "I feel better. A little sore here and there but good. I'd like to actually get up and stretch my legs."

Their staring contest lasted for a solid minute before finally Spock broke.

"You may walk to the dinning common to meet Doctor McCoy with me."

Jim tried not to let his shit-eating grin show.

Spock was too easy.

. . . . .

Being in a hospital bed was better than this, Jim decided.

"…And he asks me what those results even mean!" Bones rolled his eyes, stabbing almost violently into his salad. "I swear, these people aren't doctors – they're idiots who picked up a paper and drew on their own medical degree in crayon. It's like working with small children for god's sake! I'm a doctor, not a goddamned babysitter."

Doctor McCoy was, to say the least, upset. Ever since attending that various medical practitioner's workshops going on around the Star Fleet base, Bones had been in a sour mood. All he could do was complain bitterly to anyone who would listen, which meant of course Jim and Spock, though mostly the latter.

Oddly enough, Spock seemed happy – well not happy, because really, when was Spock ever _happy_? – to listen to Bones' stories, nodding along and asking questions at all the right parts.

The weirdest thing was that they seemed somehow used to this set-up, like the two would've been doing exactly this with or without their mutual friend and captain. For a moment, it reminded Jim that there was a time, no so terribly long ago, where he'd been out of commission. Reasonably, the two men closest to Jim had formed a sort of friendship.

Jim felt a strange stab of something in his gut.

"Earth to Jim, come in Jim," Leonard waved a hand in front of the captain's face, who at least had the grace to look embarrassed to be caught zoning out. "Did you miss everything I just asked you?"

"Uh…," Kirk trailed off, trying to think about the words that had been coming out of his friend's mouth only moment ago yet found he was drawing a blank. Instead, Jim opted for smiling winningly as his apology.

"Leonard asked if about how you are feeling," Spock supplied.

Jim paused, and then smirked, glancing between the two, "Oh? So it's 'Leonard' now?"

"Can it," Bones huffed. "Do you have any pain, any kind of stiffness?"

"Who would've thought – my first officer and chief medical officer buddying up," Jim shook his head in mock disbelief. "I think hell might've frozen over."

"Captain," Spock warned, arching his infamous eyebrow.

Jim waved the two off, "I'm fine, really. Everything's good. Sheesh, the two of you are like my den mothers or something."

Bones relaxed visibly and just nodded his head, stuffing another vicious forkful of salad into his mouth. For a moment, the three sat in companionable silence as Leonard inhaled his food with renewed purpose. Finally, the doctor spoke back up.

"Sorry to dine and dash," the southern man dabbed at the corners of his mouth, "but I've got a list of things to do as long as my arm."

Now or never – Jim took the plunge.

"How's Khan doing?" The question came out more abruptly than Jim had anticipated, wincing at its forced-sounding nature. This gave McCoy pause as he stared at his captain, understanding flashed across his features briefly.

"He's good, Jim," Leonard sighed and ran a hand over his jaw contemplatively, "Actually, I'm supposed to go give him his lunch right now and his vitamins, but strictly speaking _I _ don't have to be the one to do it. You wanna do me a favor and go in my place?"

The idea of being faced with Khan again sent a strange set of feelings jolting down Jim Kirk's spine. Anticipation, fear, gratitude, guilt, _excitement_. Khan was fascinating, as Spock would put it, and Jim felt strangely drawn to him, as well as being in debt to the man for saving his life. The least thing he could do is pop in and say thanks, no biggie.

"Sure," Jim tried for nonchalant but felt somehow like he'd missed that mark entirely, going by the way Bones grinned back at him.

Captain Kirk sprang up, feeling invigorated. At last, he could talk to Khan again, maybe get more answer, maybe ask him how the hell he knew that bomb was behind that glass, maybe even learn a little more about that supposed 'other' universe he called home.

"Captain, it would be logical to –,"

"I'll meet up with you two later," Jim tossed over his shoulder as he bounded away.

Spock and Leonard exchanged glances.

"You know, this might be the start of something great," Doctor McCoy offered with a shrug. The Vulcan turned his attention back to the other man, looking sullen.

"That is highly illogical."

. . . . .

One breath in, one breath out.

Jim's hands shook where they were holding the tray of food. In a rare display of self-consciousness, Jim Kirk actually felt nervous as he stood facing the large metal door to Khan's cell. He hadn't the faintest idea what he might say to the man other than simply thanking him and even that seemed somewhat inadequate.

This Khan had saved his life, which could be a ploy to garner his trust, but somehow Jim kept thinking back to his eyes, watching him with a starling amount of fear. That man had not appeared arrogantly scheming like the original Khan. He had seemed almost humble.

Jim opened the door.

"Hey I just wanted to –," Jim started before he could chicken out but once he fully stepped into the medical cell, it looked empty.

The captain took a moment to glance around – this cell was much roomier, and it actually had a cot plastered to the opposing wall beside another door. There was a small table next to two chairs on the right-hand side and a little stool. Altogether, the room seemed even more sterile; the walls were clinically white and illuminated brightly, near blindingly, without any windows to break the monotony.

The door facing Jim opened.

And Khan Noonien Singh stepped through, damp, shirtless, and sans handcuffs.

"Captain Kirk," surprise played across the super-soldier's features. He quickly pushed a hand through his wet locks, attempting to slick them back into shape, and reached for his neatly folded shirt lying on the cot, rapidly pulling it over his head.

But it was too late – Jim had seen.

An intricate webbing of scars decorated Khan's taut abdomen, running crosswise across his ribs along with a few, jagged and errant lines over his stomach. It was painfully obvious how the wounds had been dealt out – clean lines were a whip of some sort, unsteady lines were a knife or serrated edge, any kind of burst was blunt force trauma. Now Bones' concern made more sense – Khan had been tortured extensively with the intention to hurt, _to_ _break_.

A lesser man would have dropped the food tray.

"I brought you lunch," Jim said dumbly, glancing down at the decent-looking plated steak.

Khan's sea-gray eyes pierced him, picking apart everything about the captain as he took several poised steps forward, back ramrod straight and muscles rigid with tension. Suddenly, Jim was struck by the feeling of being an animal caretaker having just stepped into the den of a feral beast.

"Thank you," came the baritone reply. Khan ducked his head slightly as if sympathetic to Jim's nerves and reached slowly for the dish. Jim mentally kicked himself and repeated his mantra silently – _not the same, not the same, not the same._

Khan sat back on his haunches with his food in one of the two chairs, gesturing for the captain to do the equivalent. Jim stayed standing.

"It is a pleasure to see you, James Kirk," Khan balanced the tray on his knees as he delicately began cutting into the meat. Jim transfixed upon the elegant fingers moving seamlessly through the mundane motions. "I am glad to see that you are unharmed."

Jim's attention darted sharply back to Khan's face.

"Yeah?" It came out sounding more like a question. Jim cleared his throat, "I owe you a thanks, and probably a lot more than just that."

Khan noticeably grimaced as he took his first bite of the steak, politely chewing and swallowing before he answered, "You are welcome, but your gratitude is unnecessary."

"You saved my life."

The statement hung heavily in the air, and Jim was struck again by the truth of it.

"I did what most would have done and I mean this with no false-sense of modesty," Khan cut another small bite for himself. "You are alive and well, for which I am glad."

The silence stretched on uncomfortably as the prisoner continued to eat, consuming his food steadily, methodically, and undoubtedly waiting for some kind of reply from the captain. Perhaps unconsciously, Khan pulled another face as he lifted the last bit of meat into his mouth.

"You don't like it," Jim blurted out. It was not a question, but a rather ineloquent statement of fact.

"I'm sorry?" Khan set his empty tray aside with a guarded expression, but Jim caught the hint of surprise playing in those steely depths.

"If you don't like it, you could have said something." Jim wondered softly aloud, "Why didn't you say something?"

Khan hesitated briefly, "It was offered and I am not so particular that I would not eat it."

The awkwardness became palpable and not for the first time, Jim couldn't help but wonder just what exactly it is they planned to do with Khan. The man's story was extraordinary, and even if Star Fleet Command did buy into it, there was no way they're just going to turn the super solider loose. So they'd what? Keep him captive forever?

What a waste! – Jim was caught off guard by the sentiment as it scorched through him. Yet he couldn't deny how much a shame it would be to see this man wither away in a cell. Not when Jim had already seen what frightening potential Khan had.

And this man was different – this Khan and the Khan frozen in his pod were studies in contrast, starkly opposite from one another. One good and the other wayward, _evil_.

Captain Kirk sat down in the chair facing Khan and steepled his fingers as he rested his elbows atop his knees.

"I want to help you," Jim made a vague motion. "I'll need to know more about you, like for starters, what kind of meat you'd like to have."

Khan smiled, genuinely smiled, where the corners of his eyes crinkled and his entire face lit up, and loosed a low chuckle. He's handsome, Jim realized belatedly, almost harshly beautiful.

Then Khan said the last thing Jim was expecting.

"I'm actually a vegetarian."

_No, not the same at all._


	8. Chapter 7

**Author's Note: Oh. My. Gosh. I am so incredibly sorry for the delay of this story. I think, however, you'll all be happy to know that I attended the San Diego Comic Con with my friend as a genderbent Kirk and Spock! :D Anyway, yes. I know, it took me way too long to get this out to you guys, but here it is, the next chapter.**

**Thanks to everyone who has reviewed (especially mfm2885, you are seriously freaking amazing) and all my lovely followers, readers, and favoriters. Please enjoy this next chapter!**

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Chapter 7: _A Penchant for Facial Hair and Debauchery_

Commander Kirk was not pleased.

In fact, Commander Kirk found himself so incredibly displeased, he truly contemplated murdering his first officer where he stood so arrogantly straight-spined in the middle of the conn. Maybe he would instead simply delight in adding a few more scars to that perfect Vulcan body.

Temptation, temptation.

"There's really no sense in killing you," Kirk confessed, upturning his palms in a mockingly peaceable gesture. He shifted in his chair, "You're much more valuable to me alive, despite your ineptitudes, and I wouldn't like to give old Sawbones the satisfaction of finally getting that autopsy I've denied him all these years."

Spock arched an eyebrow as his lips pursed behind his well-trimmed goatee, but ever sensible, the alien remained mute.

"You let a very important guest of ours leave prematurely," the Commander continued calmly, "and I admit, I am beyond disappointed in you."

"Perhaps if you had allowed me to see to his imprisonment personally this incident would not have occurred."

Ah, but Spock could only keep his mouth shut for so long. Another reason why Kirk found his first officer invaluable – the Vulcan, despite logically knowing when he ought to remain silent, liked the gamble and played with fire. And he always did know how to call it.

"Did I grant you permission to speak, Mr. Spock?" Kirk asked rhetorically, standing from his chair. Purposefully, it sat a decent foot up from the conn's main floor, allowing the Commander to easily tower over any underlings. Yet somehow, towering over the Vulcan had always proved difficult. Even when standing beneath him, Spock managed to look down his nose at the Commander.

"Apologies, commander," those black eyes burned with an intensity so unmatched by any other. Spock's obstinate streak did always manage to bring out Kirk's sadistic one.

"Apology not accepted, lieutenant. My quarters at 1800 hours where you may _apologize_ properly," the Commander all but snarled, his patience at its limit.

Spock made a fist over his right breast and bowed deeply, though somehow even the action seemed caustic. He remained in the humbled posture, "Of course, _commander_."

With that, the Vulcan stood back up to his full height and made to stride away. He only got so far as three steps.

"_Mr. Spock_."

Commander Kirk stepped off his pedestal, approaching the tense alien with all the innocence of a murderer. Deftly, he removed a dagger from the holster at his hip, the cruel blade glinting wickedly in the light. Kirk moved easily into his Lieutenant's personal space, only inches away from the other man's stoic face.

Slowly, agonizingly, Kirk ran the flat of the blade over the Vulcan's cheek, through his facial hair, dipping dangerously down his neck until at last, the Commander stopped at Spock's throbbing jugular.

"You are…dismissed," Kirk breathed, barely above a whisper.

Mr. Spock arched one damnable eyebrow before turning on his heel and disappearing, unfazed, from the bridge.

. . . . .

"The answer is no."

Captain Kirk crossed his arms.

"I haven't even asked you yet."

Admiral Tesius didn't bother to glance up from his data PADD as he replied, deceptively calm, "I know. 'Yet' being the operative word here. But the answer is still going to be a no."

"Hear me out," Jim obstinately seated himself in the chair opposite the Admiral's desk, "Please."

The elder man paused, his gaze flicking back up to the Captain before loosing a long-suffering sigh. He set the data PADD aside.

"Shoot."

"Let me take Khan on the Enterprise –,"

"No. What did I just tell you? No way in hell."

"Listen, please." Jim did his best to sound reasonable and competent, despite his admittedly insane request. "He'd be useful to the Enterprise's mission, and it would take a lot of pressure of this base. Khan could serve aboard my ship, doing menial tasks, and you'd get an open cell, sans terrorist threats. We'd both win."

Tesius frowned, his brows furrowing. "Regardless, that man is dangerous and unpredictable. There's no way."

Jim sat back in his chair, silently surveying the Admiral's desk as he churned through his thoughts. His eyes finally settled upon a picture of a young, round-faced girl grinning straight into the camera, no older than five.

"How old?" Jim asked quietly, gesturing to the frame.

"She's married."

Kirk shot Tesius a look and the man almost smiled. Almost. The frustrated wrinkle smoothed from the Admiral's forehead as he mutely regarded the fellow officer.

"She just had her thirty-first birthday." Admiral Tesius angled the picture towards himself, his eyes softening.

"They grow up fast, I hear," Jim replied lightly.

Tesius glanced back up at Captain Kirk, "They certainly do, much faster than you could ever anticipate."

Silence enveloped the two men as Tesius moved his attention between the still-shot of his infant daughter and the captain. At last, the Admiral broke the quiet.

"You would need the board's approval to get Khan out," Tesius held up a hand to stop Jim from interrupting. He sighed again, "The best way to go about it would be to get Khan to tell us what's in that metal case and neutralize it, whatever 'it' may be. He needs to pose no immediate threat whatsoever, are we clear?"

Jim beamed, "Of course. Thank you, sir."

Admiral Tesius rolled his eyes, "Don't thank me yet, son. The board is going to have a field day with provisions, assuming they'll even approve your appeal –,"

The rest of the sentence was lost as Captain Kirk nearly bounded out the door, all long legs and perfect hair rocketing off. Youth, the Admiral scoffed, he remembered what that was like.

Admiral Tesius sighed.

. . . . .

"You're early."

Khan looked starkly at ease, possibly the most relaxed Jim had seen him since his sudden appearance. The super-soldier was stretched out across his too-short cot, his regulation grade combat boots dangling over the edge. Even the sharp bruise across his cheekbone had faded drastically, now just a sallow stain.

Jim smiled faintly, "And I bring food, vegetarian-friendly as promised, along with some vitamins on the doctor's orders."

Doctor McCoy had looked at Jim suspiciously when he asked to again be the one to take Khan his lunch and was admittedly reluctant. But Jim had a way with Bones that few did, like none did.

Khan elegantly unfolded himself and closed the distance between himself and the Captain, liberating him of the food and paper cup of supplements. Just as before, Khan seated himself in one of the two chairs facing Jim and motioned for him to take a seat as well.

This time, Jim sat down.

"You know," Khan contemplatively dredged through his salad, "I would perhaps enjoy meals more if you were to actually eat something as well."

Kirk couldn't hide his surprise, "Really?"

Those sea-gray eyes flicked up at him before Khan swallowed a mouthful of greens, his Adam's apple dipping below his clavicle briefly. It was almost hypnotic.

"Yes. It feels rather impolite to enjoy lunch by myself with you just sitting and watching."

_Huh, _Jim marveled at the idea of Khan being concerned about propriety.

Meanwhile, Khan must have taken Jim's silence to mean his declination and continued, unperturbed, "Though it may be just as well, considering you're not simply here to enjoy my company."

It was not a question. Jim met Khan's steady gaze unflinchingly, which in turn analyzed him intently, picking him apart with that frightening and fierce intelligence Jim had nearly forgotten about. Jim felt breathless under the powerful scrutiny.

"You're shrewd," the Captain smiled weakly, a thinly veiled attempt to mask his mounting apprehension.

"And you're brave," Khan shot back, blandly, "maybe bordering on foolish."

Heat stabbed Jim in his stomach, burning with the sudden strike of being caught unaware and humiliation. He simmered in reply, "How do you figure that?"

"You come, unarmed, into a cell with a man whose intentions are entirely unclear and has the strength to snap your neck like a toothpick, all in the hopes of gleaning information that may save his life," Khan said in his dark timbre, "when you yourself don't even know if it's worth saving."

Captain Kirk moved swiftly, out of his chair and standing over the prisoner in one blindly fast movement, one first raised and the other firmly curled in the collar of Khan's shirt.

Khan flinched violently, his tray of food clattering noisily to the floor.

Fear flashed in his eyes, bright and shattering, and Khan threw up his hands to defend himself though not to counterattack. His entire frame seemed to coil with such straining tension that he might just snap in two.

And it was entirely the response Jim was planning to receive.

"You're also brave," the Captain said softly, lowering his fist and releasing him. Khan looked up, the terror subsiding as he smothered it behind a collected mask. "You're scared of me because of what the other version of Jim Kirk has done to you and you worry we're alike. Whatever he's done, I can promise you we're not the same. And _that_, that fear? That's how I know you're not dangerous, and also how I know your life is one I'm willing to fight for."

The dark haired man fell silent, searching Jim's face for any hint of deception. He wouldn't find any, though, and slowly began to unwind, sagging into his chair.

"What do you want from me?" Khan asked hoarsely.

"What's in the metal case?" Jim fired back.

"An alloy, extremely rare and the only amount in existence – it's a vital component of a weapon my universe's Jim Kirk is attempting to build. I stole it and brought it here, hoping to keep it from his bloody hands," Khan heaved a great sigh, "Though I imagine you care more that the case is armed with a device set to release a deadly chemical compound to destroy the alloy should it attempt to be opened and the key code not entered within five seconds. However, given the alloy's volatile nature, destroying it will result in a large explosion."

"How large?"

Khan didn't blink, "Planet-sized."

Jim sat back down, staggered by the news.

He and the super-soldier stared at one another in mutual silence for a long moment before the captain glanced down at the scattered remnant of Khan's lunch. Guilt prickled at the base of his neck.

"I'm sorry," Jim frowned apologetically, "I shouldn't have tried to frighten you like that."

"It was…necessary," Khan glanced away uncomfortably, "You are not the Kirk I am familiar with yet I have treated you as such. A face, in no way, makes the man."

"Even one this good looking?" Kirk offered a little smile, a tentative olive branch.

Khan returned the smile.

"Yes, Captain, even one as handsome as yours."


End file.
